One of the major goals of the World Health Organization is to reduce the prevalence of TB to half by 2015, and eliminate it as a public health threat by 2050 [Dye C, et al., JAMA. 2005; 293(22):2767-75; Lonnroth K, et al., Lancet. 2010; 375(9728):1814-29]. An essential element required to achieve this goal is the development and implementation of new drugs to treat multiple drug resistant (MDR) and extensively drug resistant (XDR) tuberculosis as well as new drugs to for preventative treatment of latent M. tuberculosis infections. At present four existing drugs and six recently developed drugs are in clinical trials for their effectiveness in treating tuberculosis [Ma Z, et al., Lancet. 2010; 375(9731):2100-9] and the Global Alliance for TB Drug Development lists at least 15 additional products and drug groups in preclinical development. Although the number of compounds in the drug development pipeline is encouraging, there remain several scientific and operational impediments to their rapid introduction into treatment regimens [Ma Z, et al., Lancet. 2010; 375(9731):2100-9]. As potentially new drugs progress through the developmental pipeline, the continued emergence of MDR and XDR tuberculosis and the co-prevalence of tuberculosis with HIV add additional pressures to strained tuberculosis control programs [Harries A D, et al., Lancet. 2010; 375(9729):1906-19].
One scientific challenge noted in several reviews as an accelerator for TB drug development [Ma Z, et al., Lancet. 2010; 375(9731):2100-9; Parida S K, et al., Drug Discov Today. 2010; 15(3-4):148-57; Wallis R S, et al., Lancet. 2010; 375(9729):1920-37] and also emphasized in the FDA Office of Critical Path Programs' RFA SF424 RR is the development of “biomarkers” for cure and/or prediction of long-term outcome. The traditional endpoint of licensing trials for anti-TB drugs and regimens is cure without relapse at one to two years after the end of treatment. Thus, trials to evaluate new TB drugs commonly require two to four years to complete. Initial phases of clinical trials use two-month culture conversion and extended early bactericidal activity (EBA) assays to demonstrate sufficient efficacy to move products forward [Donald P R, et al., Tuberculosis (Edinb). 2008; 88 Suppl 1:S75-83; Ma Z, et al., Lancet. 2010; 375(9731):2100-9]. However, the requirement for long-term follow-up in Phase III trials and the use of resource and labor intensive methods such as quantitative culture/colony forming unit (CFU) assays increases the time and cost of evaluating drugs for TB treatment. The identification of biomarkers, or biosignatures, that serve as surrogate endpoints for cure would greatly enhance clinical trials by decreasing the time and cost required to determine treatment efficacy.
Biomarkers of response to TB treatment may reflect changes in the host as well as the pathogen and there are a large number of biological processes or molecules that can serve as biomarkers [Parida S K, et al., Drug Discov Today. 2010; 15(3-4):148-57]. Currently, applied diagnostic approaches that monitor the adaptive immune response of the host (T cell and antibody responses) are likely poor surrogates for the prediction of cure during the treatment of tuberculosis since the immune response is typically long-lived and can be primed by antigens released from dying or dead bacilli [Wallis R S, et al., Lancet. 2010; 375(9729):1920-37; Locht C, et al., Expert Opin Biol Ther. 2007; 7(11):1665-77; Nyendak M R, et al., Curr Opin Infect Dis. 2009; 22(2):174-82; Pai M, et al., Lancet Infect Dis. 2007; 7(6):428-38]. Likewise, the monitoring of pathogen macromolecules (antigen detection) to assess drug efficacy could vary depending on pathogen load and be prolonged as the host tries to clear the dead bacilli.
The monitoring of the transcriptome has demonstrated some success. In a study performed with sputum samples from EBA trials comparing INH, rifampin, and rifalazil and patients on standard short course chemotherapy, the levels in sputum of the M. tuberculosis fbpB (fibronectin-binding protein/85B) and hspX (alpha-crystalline homologue) declined rapidly in parallel with sputum CFU counts during treatment [Desjardin L E, et al., Am J Respir Crit Care Med. 1999; 160(1):203-10]. However, cultures remained positive after mRNAs became undetectable. A second study found that sputum icl (encoding the isocitrate lyase enzyme from the M. tuberculosis glyoxylate cycle pathway) mRNA levels correlated highly with sputum CFU during the first seven days of treatment, remained detectable after one and two months of standard TB therapy and correlated with culture positivity on solid media [Li L, et al., J Clin Microbiol. 2010; 48(1):46-51. PMCID: 2812283]. The monitoring of host gene expression profiles also revealed a diagnostic signature for patients with relapsing disease in comparison to healthy controls and active tuberculosis patients [Mistry R, et al., J Infect Dis. 2007; 195(3):357-65]. The down-sides to transcriptome monitoring are extensive sample processing and the inability to normalize data from sputum samples.
Currently, the only accepted biomarker for sterilizing activity of tuberculosis drug regimens is conversion of sputum to culture negative on solid media after two months of drug treatment [Ma Z, et al., Lancet. 2010; 375(9731):2100-9]. Thus, there is an urgent need to find alternative biomarkers that not only predict a person's response to treatment regimen but also serve as a surrogate endpoint for cure. The present invention provides such markers, fulfilling an important need in the art to allow for the assessment of the efficacy of drug treatment for tuberculosis.